bool WriteXYZ(ostream &ofs,OBMol &mol)
{
unsigned int i;
char buffer[BUFF_SIZE];
sprintf(buffer,"%d", mol.NumAtoms());
ofs << buffer << endl;
sprintf(buffer,"%s\tEnergy: %15.7f", mol.GetTitle(), mol.GetEnergy());
ofs << buffer << endl;
OBAtom *atom;
string str,str1;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
sprintf(buffer,"%3s%15.5f%15.5f%15.5f",
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs << buffer << endl;
}
return(true);
}
bool PQSFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
unsigned int i;
char buffer[BUFF_SIZE];
OBAtom *atom;
ofs<<"TEXT="<<mol.GetTitle()<<endl;
ofs<<"GEOM=PQS"<<endl;
for (i=1; i<=mol.NumAtoms(); i++)
{
atom=mol.GetAtom(i);
snprintf(buffer, BUFF_SIZE, "%s %10.6lf %10.6lf %10.6lf",
OBElements::GetSymbol(atom->GetAtomicNum()),
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs<<buffer<<endl;
}
return(true);
}
bool WriteViewMol(ostream &ofs,OBMol &mol)
{
unsigned int i;
char buffer[BUFF_SIZE];
if (strlen(mol.GetTitle()) > 0)
ofs << "$title" << endl << mol.GetTitle() << endl;
ofs << "$coord 1.0" << endl;
OBAtom *atom;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
sprintf(buffer,"%22.14f%22.14f%22.14f %s",
atom->GetX(),
atom->GetY(),
atom->GetZ(),
etab.GetSymbol(atom->GetAtomicNum()));
ofs << buffer << endl;
}
ofs << "$end" << endl;
return(true);
}
bool TurbomoleFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
double UnitConv=AAU;
if(pConv->IsOption("a"))
UnitConv=1;
ofs << "$coord" <<endl;
char buffer[BUFF_SIZE];
OBAtom *atom;
vector<OBAtom*>::iterator i;
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
char symb[8];
strcpy(symb,OBElements::GetSymbol(atom->GetAtomicNum()));
snprintf(buffer, BUFF_SIZE, "%20.14f %20.14f %20.14f %s",
atom->GetX()/UnitConv,
atom->GetY()/UnitConv,
atom->GetZ()/UnitConv,
strlwr(symb) );
ofs << buffer << endl;
}
ofs << "$end" << endl;
return true;
}
unsigned int OBRing::GetRootAtom()
{
vector<int>::iterator i;
OBMol *mol = (OBMol*)GetParent();
//if (!IsAromatic())
// return 0;
if (Size() == 6)
for (i = _path.begin();i != _path.end();++i)
if (mol->GetAtom(*i)->GetAtomicNum() != OBElements::Carbon)
return (*i);
if (Size() == 5)
for (i = _path.begin();i != _path.end();++i) {
OBAtom *atom = mol->GetAtom(*i);
switch (atom->GetAtomicNum()) {
case OBElements::Sulfur:
if (atom->GetValence() == 2)
return (*i);
break;
case OBElements::Oxygen:
if (atom->GetValence() == 2)
return (*i);
break;
case OBElements::Nitrogen:
if (atom->BOSum() == atom->GetValence())
return (*i);
break;
}
}
return 0;
}
bool JaguarInputFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL) return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
unsigned int i;
char buffer[BUFF_SIZE];
OBAtom *atom;
ofs << mol.GetTitle() << endl << endl;
ofs << "&gen" << endl;
ofs << "&" << endl;
ofs << "&zmat" << endl;
for (i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
snprintf(buffer, BUFF_SIZE, " %s%d %12.7f %12.7f %12.7f",
etab.GetSymbol(atom->GetAtomicNum()), i,
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs << buffer << endl;
}
ofs << "&" << endl;
return(true);
}
void fingerprint2::getFragments(vector<int> levels, vector<int> curfrag,
int level, OBAtom* patom, OBBond* pbond)
{
//Recursive routine to analyse schemical structure and populate fragset and ringset
//Hydrogens,charges(except dative bonds), spinMultiplicity ignored
const int Max_Fragment_Size = 7;
int bo=0;
if(pbond)
{
bo = pbond->IsAromatic() ? 5 : pbond->GetBO();
// OBAtom* pprevat = pbond->GetNbrAtom(patom);
// if(patom->GetFormalCharge() && (patom->GetFormalCharge() == -pprevat->GetFormalCharge()))
// ++bo; //coordinate (dative) bond eg C[N+]([O-])=O is seen as CN(=O)=O
}
curfrag.push_back(bo);
curfrag.push_back(patom->GetAtomicNum());
levels[patom->GetIdx()-1] = level;
vector<OBEdgeBase*>::iterator itr;
OBBond *pnewbond;
// PrintFpt(curfrag,(int)patom);
for (pnewbond = patom->BeginBond(itr);pnewbond;pnewbond = patom->NextBond(itr))
{
if(pnewbond==pbond) continue; //don't retrace steps
OBAtom* pnxtat = pnewbond->GetNbrAtom(patom);
if(pnxtat->GetAtomicNum() == OBElements::Hydrogen) continue;
int atlevel = levels[pnxtat->GetIdx()-1];
if(atlevel) //ring
{
if(atlevel==1)
{
//If complete ring (last bond is back to starting atom) add bond at front
//and save in ringset
curfrag[0] = pnewbond->IsAromatic() ? 5 : pnewbond->GetBO();
ringset.insert(curfrag);
curfrag[0] = 0;
}
}
else //no ring
{
if(level<Max_Fragment_Size)
{
// TRACE("level=%d size=%d %p frag[0]=%p\n",level, curfrag.size(),&curfrag, &(curfrag[0]));
//Do the next atom; levels, curfrag are passed by value and hence copied
getFragments(levels, curfrag, level+1, pnxtat, pnewbond);
}
}
}
//do not save C,N,O single atom fragments
if(curfrag[0]==0 &&
(level>1 || patom->GetAtomicNum()>8 || patom->GetAtomicNum()<6))
{
fragset.insert(curfrag); //curfrag ignored if an identical fragment already present
// PrintFpt(curfrag,level);
}
}
static void WriteMolFile(OBMol* pmol, OBConversion* pconv, OBFormat* pformat)
{
ostream &ofs = *pconv->GetOutStream();
ofs << "$MOL" << '\n';
// Treat a dummy atom with "rxndummy" as the empty file
if (pmol->NumAtoms() == 1) {
OBAtom *atm = pmol->GetFirstAtom();
if (atm->GetAtomicNum() == 0 && atm->HasData("rxndummy"))
pmol->DeleteAtom(atm);
}
pformat->WriteMolecule(pmol, pconv);
}
bool WriteGromos96(ostream &ofs,OBMol &mol,double fac)
{
char type_name[10];
char res_name[10],padded_name[10];
char buffer[BUFF_SIZE];
int res_num;
sprintf(buffer,"#GENERATED BY OPEN BABEL %s",BABEL_VERSION);
ofs << buffer << endl;
/* GROMOS wants a TITLE block, so let's write one*/
sprintf(buffer,"TITLE\n%s\nEND",mol.GetTitle());
ofs << buffer << endl;
ofs << "POSITION" << endl;
OBAtom *atom;
OBResidue *res;
vector<OBNodeBase*>::iterator i;
for(atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
if (res = atom->GetResidue())
{
strcpy(res_name,(char*)res->GetName().c_str());
strcpy(type_name,(char*)res->GetAtomID(atom).c_str());
res_num = res->GetNum();
}
else
{
strcpy(type_name,etab.GetSymbol(atom->GetAtomicNum()));
strcpy(res_name,"UNK");
sprintf(padded_name,"%2s",type_name);
strcpy(type_name,padded_name);
res_num = 1;
}
sprintf(buffer,"%5d %5s %5s %6d %15.5f %15.5f %15.5f",
res_num,res_name,type_name,atom->GetIdx(),
atom->x()*fac,atom->y()*fac,atom->z()*fac);
ofs << buffer << endl;
if (!(atom->GetIdx()%10))
{
sprintf(buffer,"# %d",atom->GetIdx());
ofs << buffer << endl;
}
}
ofs << "END" << endl;
return(true);
}
void ChemDrawXMLFormat::EnsureEndElement(void)
{
if (_tempAtom.GetAtomicNum() != 0)
{
_pmol->AddAtom(_tempAtom);
atoms[_tempAtom.GetIdx()] = _pmol->NumAtoms();
_tempAtom.Clear();
}
else if (Order >= 0)
{
_pmol->AddBond(Begin, End, Order, Flag);
Order = -1;
}
}
void WriteCharges(ostream &ofs,OBMol &mol)
{
unsigned int i;
OBAtom *atom;
char buffer[BUFF_SIZE];
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
sprintf(buffer,"%4s%4d % 2.10f",
etab.GetSymbol(atom->GetAtomicNum()),
i,
atom->GetPartialCharge());
ofs << buffer << endl;
}
}
void ReportFormat::WriteCharges(ostream &ofs,OBMol &mol)
{
unsigned int i;
OBAtom *atom;
char buffer[BUFF_SIZE];
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
snprintf(buffer, BUFF_SIZE, "%4s%4d % 2.10f",
OBElements::GetSymbol(atom->GetAtomicNum()),
i,
atom->GetPartialCharge());
ofs << buffer << "\n";
}
}
void WriteChiral(ostream &ofs,OBMol &mol)
{
OBAtom *atom;
vector<OBNodeBase*>::iterator i;
char buffer[BUFF_SIZE];
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
if (atom->IsChiral())
{
sprintf(buffer,"%4s %5d is chiral: %s",
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetIdx(),
(atom->IsClockwise() ? "clockwise" : "counterclockwise"));
ofs << buffer << endl;
}
}
}
bool CacaoFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
OBAtom *atom;
char buffer[BUFF_SIZE];
vector<OBAtom*>::iterator i;
snprintf(buffer, BUFF_SIZE, "%s\n",mol.GetTitle());
ofs << buffer;
snprintf(buffer, BUFF_SIZE, "%3d DIST 0 0 0\n",mol.NumAtoms());
ofs << buffer;
if (!mol.HasData(OBGenericDataType::UnitCell))
ofs << "CELL 1.,1.,1.,90.,90.,90.\n";
else
{
OBUnitCell *uc = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
snprintf(buffer, BUFF_SIZE, "CELL %f,%f,%f,%f,%f,%f\n",
uc->GetA(), uc->GetB(), uc->GetC(),
uc->GetAlpha(), uc->GetBeta(), uc->GetGamma());
ofs << buffer;
}
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
snprintf(buffer,BUFF_SIZE,"%2s %7.4f, %7.4f, %7.4f\n",
etab.GetSymbol(atom->GetAtomicNum()),
atom->x(),
atom->y(),
atom->z());
ofs << buffer;
}
return(true);
}
bool fingerprint2::GetFingerprint(OBBase* pOb, vector<unsigned int>&fp, int nbits)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(!pmol) return false;
fp.resize(1024/Getbitsperint());
fragset.clear();//needed because now only one instance of fp class
ringset.clear();
//identify fragments starting at every atom
OBAtom *patom;
vector<OBNodeBase*>::iterator i;
for (patom = pmol->BeginAtom(i);patom;patom = pmol->NextAtom(i))
{
if(patom->GetAtomicNum() == OBElements::Hydrogen) continue;
vector<int> curfrag;
vector<int> levels(pmol->NumAtoms());
getFragments(levels, curfrag, 1, patom, NULL);
}
// TRACE("%s %d frags before; ",pmol->GetTitle(),fragset.size());
//Ensure that each chemically identical fragment is present only in a single
DoRings();
DoReverses();
SetItr itr;
_ss.str("");
for(itr=fragset.begin();itr!=fragset.end();++itr)
{
//Use hash of fragment to set a bit in the fingerprint
int hash = CalcHash(*itr);
SetBit(fp,hash);
if(!(Flags() & FPT_NOINFO))
PrintFpt(*itr,hash);
}
if(nbits)
Fold(fp, nbits);
// TRACE("%d after\n",fragset.size());
return true;
}
bool WriteHIN(ostream &ofs,OBMol &mol)
{
unsigned int i, file_num = 1;
string str,str1;
char buffer[BUFF_SIZE];
OBAtom *atom;
OBBond *bond;
vector<OBEdgeBase*>::iterator j;
char bond_char;
ofs << "mol " << file_num << " " << mol.GetTitle() << endl;;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
sprintf(buffer,"atom %d - %-3s ** - %8.5f %8.5f %8.5f %8.5f %d ",
i,
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetPartialCharge(),
atom->GetX(),
atom->GetY(),
atom->GetZ(),
atom->GetValence());
ofs << buffer;
for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))
{
switch(bond->GetBO())
{
case 1 : bond_char = 's'; break;
case 2 : bond_char = 'd'; break;
case 3 : bond_char = 't'; break;
case 5 : bond_char = 'a'; break;
default: bond_char = 's'; break;
}
sprintf(buffer,"%d %c ", (bond->GetNbrAtom(atom))->GetIdx(), bond_char);
ofs << buffer;
}
ofs << endl;
}
ofs << "endmol " << file_num << endl;
return(true);
}
bool WriteFeat(ostream &ofs,OBMol &mol)
{
char buffer[BUFF_SIZE];
ofs << mol.NumAtoms() << endl;
ofs << mol.GetTitle() << endl;
OBAtom *atom;
vector<OBNodeBase*>::iterator i;
for(atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
sprintf(buffer,"%-3s %8.5f %8.5f %8.5f ",
etab.GetSymbol(atom->GetAtomicNum()),
atom->x(),
atom->y(),
atom->z());
ofs << buffer << endl;
}
return(true);
}
void OutputAtoms(ostream &ofs, OBMol &mol, string prefix)
{
/* ---- Write all coordinates ---- */
ofs << "//Coodinates of atoms 1 - " << mol.NumAtoms() << endl;
unsigned int i;
for(i = 1; i <= mol.NumAtoms(); ++i)
{
/* ---- Get a pointer to ith atom ---- */
OBAtom *atom = mol.GetAtom(i);
/* ---- Write position of atom i ---- */
ofs << "#declare " << prefix << "_pos_" << i << " = <"
<< atom -> GetX() << ","
<< atom -> GetY() << ","
<< atom -> GetZ()
<< ">;" << endl;
}
/* ---- Write povray-description of all atoms ---- */
ofs << endl << "//Povray-description of atoms 1 - " << mol.NumAtoms() << endl;
for(i = 1; i <= mol.NumAtoms(); ++i)
{
/* ---- Get a pointer to ith atom ---- */
OBAtom *atom = mol.GetAtom(i);
/* ---- Write full description of atom i ---- */
ofs << "#declare " << prefix << "_atom" << i << " = ";
ofs << "object {" << endl
<< "\t Atom_" << etab.GetSymbol(atom->GetAtomicNum()) << endl
<< "\t translate " << prefix << "_pos_" << i << endl << "\t }" << endl;
}
/* ---- Add empty line ---- */
ofs << endl;
}
//copy data needed to write out pmol from obmol
void PMolCreator::copyFrom(OBMol& mol, bool deleteH)
{
static OBIsotopeTable isotable;
name = mol.GetTitle();
//first construct atoms
int typeindex[256]; //position in atoms vector of an atom type, indexed by atomic number
int tmpatomindex[mol.NumAtoms()]; //position within the atom type vector
memset(typeindex, -1, sizeof(typeindex));
memset(tmpatomindex, -1, sizeof(tmpatomindex));
for (OBAtomIterator aitr = mol.BeginAtoms(); aitr != mol.EndAtoms(); ++aitr)
{
OBAtom *atom = *aitr;
unsigned int idx = atom->GetIdx();
unsigned anum = atom->GetAtomicNum();
assert(anum < 256);
if(deleteH && anum == 1)
continue;
int pos = typeindex[anum];
if (pos < 0) // no vector for this type yet
{
pos = typeindex[anum] = atoms.size();
atoms.push_back(AtomGroup(anum));
}
tmpatomindex[idx] = atoms[pos].coords.size();
atoms[pos].coords.push_back(FloatCoord(atom->x(), atom->y(), atom->z()));
}
//create mapping to actual atom index
numAtoms = 0;
BOOST_FOREACH(AtomGroup& ag, atoms)
{ ag.startIndex = numAtoms;
numAtoms += ag.coords.size();
}
bool TinkerFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
bool mm2Types = false;
bool mmffTypes = pConv->IsOption("m",OBConversion::OUTOPTIONS) != NULL;
bool mm3Types = pConv->IsOption("3",OBConversion::OUTOPTIONS) != NULL;
bool classTypes = pConv->IsOption("c", OBConversion::OUTOPTIONS) != NULL;
unsigned int i;
char buffer[BUFF_SIZE];
OBBond *bond;
vector<OBBond*>::iterator j;
// Before we try output of MMFF94 atom types, check if it works
OBForceField *ff = OpenBabel::OBForceField::FindForceField("MMFF94");
if (mmffTypes && ff && ff->Setup(mol))
mmffTypes = ff->GetAtomTypes(mol);
else
mmffTypes = false; // either the force field isn't available, or it doesn't work
if (!mmffTypes && !mm3Types && !classTypes) {
snprintf(buffer, BUFF_SIZE, "%6d %-20s MM2 parameters\n",mol.NumAtoms(),mol.GetTitle());
mm2Types = true;
}
else if (mm3Types)
snprintf(buffer, BUFF_SIZE, "%6d %-20s MM3 parameters\n",mol.NumAtoms(),mol.GetTitle());
else if (classTypes)
snprintf(buffer, BUFF_SIZE, "%6d %-20s Custom parameters\n",mol.NumAtoms(),mol.GetTitle());
else
snprintf(buffer, BUFF_SIZE, "%6d %-20s MMFF94 parameters\n",mol.NumAtoms(),mol.GetTitle());
ofs << buffer;
ttab.SetFromType("INT");
OBAtom *atom;
string str,str1;
int atomType;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
str = atom->GetType();
atomType = 0; // Something is very wrong if this doesn't get set below
if (mm2Types) {
ttab.SetToType("MM2");
ttab.Translate(str1,str);
atomType = atoi((char*)str1.c_str());
}
if (mmffTypes) {
// Override the MM2 typing
OBPairData *type = (OpenBabel::OBPairData*)atom->GetData("FFAtomType");
if (type) {
str1 = type->GetValue().c_str();
atomType = atoi((char*)str1.c_str());
}
}
if (mm3Types) {
// convert to integer for MM3 typing
atomType = SetMM3Type(atom);
}
if (classTypes) {
// Atom classes are set by the user, so use those
OBGenericData *data = atom->GetData("Atom Class");
if (data) {
OBPairInteger* acdata = dynamic_cast<OBPairInteger*>(data); // Could replace with C-style cast if willing to live dangerously
if (acdata) {
int ac = acdata->GetGenericValue();
if (ac >= 0)
atomType = ac;
}
}
}
snprintf(buffer, BUFF_SIZE, "%6d %2s %12.6f%12.6f%12.6f %5d",
i,
OBElements::GetSymbol(atom->GetAtomicNum()),
atom->GetX(),
atom->GetY(),
atom->GetZ(),
atomType);
ofs << buffer;
for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))
{
snprintf(buffer, BUFF_SIZE, "%6d", (bond->GetNbrAtom(atom))->GetIdx());
ofs << buffer;
}
ofs << endl;
}
return(true);
}
bool MOL2Format::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
bool ligandsOnly = pConv->IsOption("l", OBConversion::OUTOPTIONS)!=NULL;
//The old code follows....
string str,str1;
char buffer[BUFF_SIZE],label[BUFF_SIZE];
char rnum[BUFF_SIZE],rlabel[BUFF_SIZE];
ofs << "@<TRIPOS>MOLECULE" << endl;
str = mol.GetTitle();
if (str.empty())
ofs << "*****" << endl;
else
ofs << str << endl;
snprintf(buffer, BUFF_SIZE," %d %d 0 0 0", mol.NumAtoms(),mol.NumBonds());
ofs << buffer << endl;
ofs << "SMALL" << endl;
OBPairData *dp = (OBPairData*)mol.GetData("PartialCharges");
if (dp != NULL) {
// Tripos spec says:
// NO_CHARGES, DEL_RE, GASTEIGER, GAST_HUCK, HUCKEL, PULLMAN,
// GAUSS80_CHARGES, AMPAC_CHARGES, MULLIKEN_CHARGES, DICT_ CHARGES,
// MMFF94_CHARGES, USER_CHARGES
if (dp->GetValue() == "Mulliken")
ofs << "MULLIKEN_CHARGES" << endl;
else // should pick from the Tripos types
ofs << "GASTEIGER" << endl;
}
else { // No idea what these charges are... all our code sets "PartialCharges"
ofs << "GASTEIGER" << endl;
}
ofs << "Energy = " << mol.GetEnergy() << endl;
if (mol.HasData(OBGenericDataType::CommentData))
{
OBCommentData *cd = (OBCommentData*)mol.GetData(OBGenericDataType::CommentData);
ofs << cd->GetData();
}
ofs << endl;
ofs << "@<TRIPOS>ATOM" << endl;
OBAtom *atom;
OBResidue *res;
vector<OBAtom*>::iterator i;
vector<int> labelcount;
labelcount.resize( etab.GetNumberOfElements() );
ttab.SetFromType("INT");
ttab.SetToType("SYB");
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
//
// Use sequentially numbered atom names if no residues
//
snprintf(label,BUFF_SIZE, "%s%d",
etab.GetSymbol(atom->GetAtomicNum()),
++labelcount[atom->GetAtomicNum()]);
strcpy(rlabel,"<1>");
strcpy(rnum,"1");
str = atom->GetType();
ttab.Translate(str1,str);
//
// Use original atom names if there are residues
//
if (!ligandsOnly && (res = atom->GetResidue()) )
{
// use original atom names defined by residue
snprintf(label,BUFF_SIZE,"%s",(char*)res->GetAtomID(atom).c_str());
// make sure that residue name includes its number
snprintf(rlabel,BUFF_SIZE,"%s%d",res->GetName().c_str(), res->GetNum());
snprintf(rnum,BUFF_SIZE,"%d",res->GetNum());
}
snprintf(buffer,BUFF_SIZE,"%7d%1s%-6s%12.4f%10.4f%10.4f%1s%-5s%4s%1s %-8s%10.4f",
atom->GetIdx(),"",label,
atom->GetX(),atom->GetY(),atom->GetZ(),
"",str1.c_str(),
rnum,"",rlabel,
atom->GetPartialCharge());
ofs << buffer << endl;
}
ofs << "@<TRIPOS>BOND" << endl;
OBBond *bond;
vector<OBBond*>::iterator j;
OBSmartsPattern pat;
string s1, s2;
for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
{
s1 = bond->GetBeginAtom()->GetType();
s2 = bond->GetEndAtom()->GetType();
if (bond->IsAromatic() || s1 == "O.co2" || s2 == "O.co2")
strcpy(label,"ar");
else if (bond->IsAmide())
strcpy(label,"am");
else
snprintf(label,BUFF_SIZE,"%d",bond->GetBO());
snprintf(buffer, BUFF_SIZE,"%6d%6d%6d%3s%2s",
bond->GetIdx()+1,bond->GetBeginAtomIdx(),bond->GetEndAtomIdx(),
"",label);
ofs << buffer << endl;
}
// NO trailing blank line (PR#1868929).
// ofs << endl;
return(true);
}
bool HINFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
unsigned int i, file_num = 1;
string str,str1;
char buffer[BUFF_SIZE];
OBAtom *atom;
OBBond *bond;
vector<OBBond*>::iterator j;
char bond_char;
// make sure to escape titles in double quotes
// PR#1501694
ofs << "mol " << file_num << " \"" << mol.GetTitle() << "\"\n";
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
snprintf(buffer, BUFF_SIZE, "atom %d - %-3s ** - %8.5f %8.5f %8.5f %8.5f %d ",
i,
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetPartialCharge(),
atom->GetX(),
atom->GetY(),
atom->GetZ(),
atom->GetValence());
ofs << buffer;
for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))
{
switch(bond->GetBO())
{
case 1 :
bond_char = 's';
break;
case 2 :
bond_char = 'd';
break;
case 3 :
bond_char = 't';
break;
case 5 :
bond_char = 'a';
break;
default:
bond_char = 's';
break;
}
if (bond->IsAromatic())
bond_char = 'a';
snprintf(buffer,BUFF_SIZE, "%d %c ", (bond->GetNbrAtom(atom))->GetIdx(), bond_char);
ofs << buffer;
}
ofs << endl;
}
ofs << "endmol " << file_num << endl;
return(true);
}
int SetMM3Type(OBAtom *atom)
{
OBAtom *b; // neighbor
OBBondIterator i, j;
int countNeighborO, countNeighborS, countNeighborN, countNeighborC;
countNeighborO = countNeighborS = countNeighborN = countNeighborC = 0;
// The MM2 typing isn't very good, so we do this ourselves for the most common atom types
switch (atom->GetAtomicNum()) {
case 1: // Hydrogen
b = atom->BeginNbrAtom(j);
if (b->IsCarboxylOxygen())
return 24;
if (b->GetAtomicNum() == OBElements::Sulfur)
return 44;
if (b->GetAtomicNum() == OBElements::Nitrogen) {
if (b->IsAmideNitrogen())
return 28;
if (b->GetValence() > 3)
return 48;// ammonium
return 23; // default amine/imine
}
if (b->GetAtomicNum() == OBElements::Carbon && b->GetHyb() == 1)
return 124; // acetylene
if (b->GetAtomicNum() == OBElements::Oxygen) {
if (b->HasAlphaBetaUnsat())
return 73; // includes non-enol/phenol, but has the right spirit
return 21; // default alcohol
}
return 5; // default H
break;
case 2: // Helium
return 51; break;
case 3: // Li
return 163; break;
case 5: // B
if (atom->GetValence() >= 4)
return 27; // tetrahedral
return 26; break;
case 6: // C
if (atom->IsInRingSize(3)) { // cyclopropane / cyclopropene
if (atom->GetHyb() == 3)
return 22;
if (atom->GetHyb() == 2) {
if (atom->CountFreeOxygens() == 1) // propanone
return 67;
return 38; // propane
}
}
if (atom->IsInRingSize(4)) { // cyclobutane or cyclobutene
if (atom->GetHyb() == 3)
return 56;
if (atom->GetHyb() == 2) {
if (atom->CountFreeOxygens() == 1) // butanone
return 58;
return 57; // regular cyclobutane
}
}
if (atom->CountBondsOfOrder(2) == 2) { // allene
if (atom->CountFreeOxygens() == 1) // ketene
return 106;
return 68;
}
if (atom->GetFormalCharge() == +1)
return 30;
if (atom->GetSpinMultiplicity() == 2)
return 29;
if (atom->GetHyb() == 3)
return 1;
else if (atom->GetHyb() == 2) {
if (atom->CountFreeOxygens() >= 1)
return 3;
return 2;
}
else if (atom->GetHyb() == 1)
return 4;
break;
case 7: // N
// TODO
if (atom->IsAmideNitrogen())
return 151;
if (atom->IsAromatic()) {
if (atom->GetFormalCharge() == 1)
return 111;
if (atom->IsInRingSize(5)) // pyrrole
return 40;
if (atom->IsInRingSize(6)) // pyridine
return 37;
}
if (atom->CountFreeOxygens() == 2) // nitro
return 46;
if (atom->GetHyb() == 3) {
if (atom->GetValence() > 3)
return 39; // ammonium
return 8;
}
else if (atom->GetHyb() == 2)
return 9;
else if (atom->GetHyb() == 1)
return 10;
break;
case 8: // O
//TODO
if (atom->IsPhosphateOxygen())
return 159;
if (atom->IsCarboxylOxygen())
return 75;
if (atom->IsInRingSize(3))
return 49; // epoxy
b = atom->BeginNbrAtom(j);
if (atom->HasBondOfOrder(2) && b->GetAtomicNum() == OBElements::Carbon) { // O=C
return 7;
}
if (atom->IsAromatic())
return 41; // furan
return 6;
break;
case 9: // F
return 11; break;
case 10: // Ne
return 52; break;
case 12: // Mg
return 59; break;
case 14: // Si
return 19; break;
case 15: // P
if (atom->CountFreeOxygens() > 0)
return 153; // phosphate
if (atom->BOSum() > 3)
return 60; // phosphorus V
return 25; break;
case 16: // S
if (atom->IsAromatic())
return 42; // thiophene
if (atom->GetFormalCharge() == 1)
return 16; // sulfonium
// look at the neighbors
for (b = atom->BeginNbrAtom(j); b; b = atom->NextNbrAtom(j))
{
switch (b->GetAtomicNum()) {
case 6:
if (b->GetHyb() == 2) // S=C
countNeighborC++; break;
case 7:
countNeighborN++; break;
case 8:
if (b->GetHvyValence() == 1)
countNeighborO++;
break;
case 16:
countNeighborS++; break;
default:
continue;
}
}
if (countNeighborO == 1)
return 17; // sulfoxide
if (countNeighborO >= 2) {
if (countNeighborN)
return 154; // sulfonamide
return 18; // sulfone or sulfate
}
if (countNeighborC)
return 74; // S=C
if (countNeighborS == 1)
return 104; // S-S disulfide
else if (countNeighborS > 1)
return 105;
return 15; break;
case 17: // Cl
return 12; break;
case 18: // Ar
return 153; break;
case 20: // Ca
return 125; break;
case 26: // Fe
if (atom->GetFormalCharge() == 2)
return 61;
return 62; break;
case 27: // Co
if (atom->GetFormalCharge() == 2)
return 65;
return 66; break;
case 28: // Ni
if (atom->GetFormalCharge() == 2)
return 63;
return 64; break;
case 32: // Ge
return 31; break;
case 34: // Se
return 34; break;
case 35: // Br
return 13; break;
case 36: // Kr
return 54; break;
case 38: // Sr
return 126; break;
case 50: // Sn
return 32; break;
case 52: // Te
return 35; break;
case 53: // I
return 14; break;
case 54: // Xe
return 55; break;
case 56: // Ba
return 127; break;
case 57:
return 128; break;
case 58:
return 129; break;
case 59:
return 130; break;
case 60:
return 131; break;
case 61:
return 132; break;
case 62:
return 133; break;
case 63:
return 134; break;
case 64:
return 135; break;
case 65:
return 136; break;
case 66:
return 137; break;
case 67:
return 138; break;
case 68:
return 139; break;
case 69:
return 140; break;
case 70:
return 141; break;
case 71:
return 142; break;
case 82: // Pb
return 33; break;
default:
break;
}
return 0;
}
bool GROMOS96Format::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
double fac = pConv->IsOption("n") ? 0.1 : 1.0; //new framework
char type_name[16];
char res_name[16];
char buffer[BUFF_SIZE];
string res_num;
snprintf(buffer, BUFF_SIZE, "#GENERATED BY OPEN BABEL %s\n",BABEL_VERSION);
ofs << buffer;
/* GROMOS wants a TITLE block, so let's write one*/
ofs << "TITLE\n" << mol.GetTitle() << "\nEND\n";
ofs << "POSITION\n";
OBAtom *atom;
OBResidue *res;
vector<OBAtom*>::iterator i;
for(atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
if ( (res = atom->GetResidue()) )
{
// 16 = sizeof(res_name) and sizeof(type_name)
strncpy(res_name,(char*)res->GetName().c_str(), 16);
res_name[15] = '\0';
strncpy(type_name,(char*)res->GetAtomID(atom).c_str(), 16);
type_name[15] = '\0';
res_num = res->GetNumString();
}
else
{
strncpy(type_name,OBElements::GetSymbol(atom->GetAtomicNum()), 16);
strcpy(res_name,"UNK");
res_num = "1";
}
snprintf(buffer, BUFF_SIZE, "%5s %5s %5s %6d %15.5f %15.5f %15.5f\n",
res_num.c_str(),res_name,type_name,atom->GetIdx(),
atom->x()*fac,atom->y()*fac,atom->z()*fac);
ofs << buffer;
if (!(atom->GetIdx()%10))
{
snprintf(buffer, BUFF_SIZE, "# %d\n",atom->GetIdx());
ofs << buffer;
}
}
ofs << "END\n";
return(true);
}
bool TinkerFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
bool mmffTypes = pConv->IsOption("m",OBConversion::OUTOPTIONS) != NULL;
unsigned int i;
char buffer[BUFF_SIZE];
OBBond *bond;
vector<OBBond*>::iterator j;
// Before we try output of MMFF94 atom types, check if it works
OBForceField *ff = OpenBabel::OBForceField::FindForceField("MMFF94");
if (mmffTypes && ff && ff->Setup(mol))
mmffTypes = ff->GetAtomTypes(mol);
else
mmffTypes = false; // either the force field isn't available, or it doesn't work
if (!mmffTypes)
snprintf(buffer, BUFF_SIZE, "%6d %-20s MM2 parameters\n",mol.NumAtoms(),mol.GetTitle());
else
snprintf(buffer, BUFF_SIZE, "%6d %-20s MMFF94 parameters\n",mol.NumAtoms(),mol.GetTitle());
ofs << buffer;
ttab.SetFromType("INT");
OBAtom *atom;
string str,str1;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
str = atom->GetType();
ttab.SetToType("MM2");
ttab.Translate(str1,str);
if (mmffTypes) {
// Override the MM2 typing
OBPairData *type = (OpenBabel::OBPairData*)atom->GetData("FFAtomType");
if (type)
str1 = type->GetValue().c_str();
}
snprintf(buffer, BUFF_SIZE, "%6d %2s %12.6f%12.6f%12.6f %5d",
i,
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetX(),
atom->GetY(),
atom->GetZ(),
atoi((char*)str1.c_str()));
ofs << buffer;
for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))
{
snprintf(buffer, BUFF_SIZE, "%6d", (bond->GetNbrAtom(atom))->GetIdx());
ofs << buffer;
}
ofs << endl;
}
return(true);
}
//! \return whether partial charges were successfully assigned to this molecule
bool EQEqCharges::ComputeCharges(OBMol &mol)
{
int i, j, a, c, N = mol.NumAtoms();
double cellVolume;
VectorXf chi(N), J(N), b(N), x(N);
MatrixXf J_ij(N, N), A(N, N);
OBUnitCell *obuc;
matrix3x3 unitcell, fourier;
vector3 dx;
int numNeighbors[3];
OBAtom *atom;
// If parameters have not yet been loaded, do that
if (!_paramFileLoaded)
{
if (ParseParamFile())
{
_paramFileLoaded = true;
} else
{
return false;
}
}
// Calculate atomic properties based around their ionic charge
for (i = 0; i < N; i++)
{
atom = mol.GetAtom(i + 1);
a = atom->GetAtomicNum();
c = _chargeCenter[a];
// Fail if ionization data is missing for any atom in the molecule
if (_ionizations[a][c + 1] == -1 || _ionizations[a][c] == -1 || a > TABLE_OF_ELEMENTS_SIZE)
{
obErrorLog.ThrowError(__FUNCTION__, "Insufficient ionization data for atoms in the given molecule. Update `data/eqeqIonizations.txt` with missing information and re-run this function.", obError);
return false;
}
J(i) = _ionizations[a][c + 1] - _ionizations[a][c];
chi(i) = 0.5 * (_ionizations[a][c + 1] + _ionizations[a][c]) - (a == 1? 0 : c * J(i));
}
// If a unit cell is defined, use the periodic Ewald calculation
if (mol.HasData(OBGenericDataType::UnitCell))
{
// Get unit cell and calculate its Fourier transform + volume
obuc = (OBUnitCell *) mol.GetData(OBGenericDataType::UnitCell);
unitcell = obuc->GetCellMatrix();
fourier = (2 * PI * unitcell.inverse()).transpose();
cellVolume = obuc->GetCellVolume();
// Get the number of radial unit cells to use in x, y, and z
numNeighbors[0] = int(ceil(minCellLength / (2.0 * (obuc->GetA())))) - 1;
numNeighbors[1] = int(ceil(minCellLength / (2.0 * (obuc->GetB())))) - 1;
numNeighbors[2] = int(ceil(minCellLength / (2.0 * (obuc->GetC())))) - 1;
for (i = 0; i < N; i++)
{
atom = mol.GetAtom(i + 1);
for (j = 0; j < N; j++)
{
dx = atom->GetVector() - (mol.GetAtom(j + 1))->GetVector();
J_ij(i, j) = GetPeriodicEwaldJij(J(i), J(j), dx, (i == j), unitcell, fourier, cellVolume, numNeighbors);
}
}
// If no unit cell, use the simplified nonperiodic calculation
} else
{
for (i = 0; i < N; i++)
{
atom = mol.GetAtom(i + 1);
for (j = 0; j < N; j++)
{
J_ij(i, j) = GetNonperiodicJij(J(i), J(j), atom->GetDistance(j + 1), (i == j));
}
return false;
}
}
// Formulate problem as A x = b, where x is the calculated partial charges
// First equation is a simple overall balance: sum(Q) = 0
A.row(0) = VectorXf::Ones(N);
b(0) = 0;
// Remaining equations are based off of the fact that, at equilibrium, the
// energy of the system changes equally for a change in any charge:
// dE/dQ_1 = dE/dQ_2 = ... = dE/dQ_N
A.block(1, 0, N - 1, N) = J_ij.block(0, 0, N - 1, N) - J_ij.block(1, 0, N - 1, N);
b.tail(N - 1) = chi.tail(N - 1) - chi.head(N - 1);
// The solution is a list of charges in the system
x = A.colPivHouseholderQr().solve(b);
// Now we are done calculating, pass all this back to OpenBabel molecule
mol.SetPartialChargesPerceived();
OBPairData *dp = new OBPairData;
dp->SetAttribute("PartialCharges");
dp->SetValue("EQEq");
dp->SetOrigin(perceived);
mol.SetData(dp);
m_partialCharges.clear();
m_partialCharges.reserve(N);
m_formalCharges.clear();
m_formalCharges.reserve(N);
for (i = 0; i < N; i ++)
{
atom = mol.GetAtom(i + 1);
atom->SetPartialCharge(x(i));
m_partialCharges.push_back(x(i));
m_formalCharges.push_back(atom->GetFormalCharge());
}
obErrorLog.ThrowError(__FUNCTION__, "EQEq charges successfully assigned.", obInfo);
return true;
}
bool PDBFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
unsigned int i;
char buffer[BUFF_SIZE];
char type_name[10], padded_name[10];
char the_res[10];
char the_chain = ' ';
const char *element_name;
int res_num;
bool het=true;
int model_num = 0;
if (!pConv->IsLast() || pConv->GetOutputIndex() > 1)
{ // More than one molecule record
model_num = pConv->GetOutputIndex(); // MODEL 1-based index
snprintf(buffer, BUFF_SIZE, "MODEL %8d", model_num);
ofs << buffer << endl;
}
// write back all fields (REMARKS, HELIX, SHEET, SITE, ...)
bool compndWritten = false;
bool authorWritten = false;
std::vector<OBGenericData*> pairData = mol.GetAllData(OBGenericDataType::PairData);
for (std::vector<OBGenericData*>::iterator data = pairData.begin(); data != pairData.end(); ++data) {
OBPairData *pd = static_cast<OBPairData*>(*data);
string attr = pd->GetAttribute();
// filter to make sure we are writing pdb fields only
if (attr != "HEADER" && attr != "OBSLTE" && attr != "TITLE" && attr != "SPLIT" &&
attr != "CAVEAT" && attr != "COMPND" && attr != "SOURCE" && attr != "KEYWDS" &&
attr != "EXPDTA" && attr != "NUMMDL" && attr != "MDLTYP" && attr != "AUTHOR" &&
attr != "REVDAT" && attr != "SPRSDE" && attr != "JRNL" && attr != "REMARK" &&
attr != "DBREF" && attr != "DBREF1" && attr != "DBREF2" && attr != "SEQADV" &&
attr != "SEQRES" && attr != "MODRES" && attr != "HET" && attr != "HETNAM" &&
attr != "HETSYN" && attr != "FORMUL" && attr != "HELIX" && attr != "SHEET" &&
attr != "SSBOND" && attr != "LINK" && attr != "CISPEP" && attr != "SITE" &&
attr != "ORIGX1" && attr != "ORIGX2" && attr != "ORIGX3" && attr != "SCALE1" &&
attr != "SCALE2" && attr != "SCALE3" && attr != "MATRIX1" && attr != "MATRIX2" &&
attr != "MATRIX3" && attr != "MODEL")
continue;
if (attr == "COMPND")
compndWritten = true;
if (attr == "AUTHOR")
authorWritten = true;
// compute spacing needed. HELIX, SITE, HET, ... are trimmed when reading
int nSpacing = 6 - attr.size();
for (int i = 0; i < nSpacing; ++i)
attr += " ";
std::string lines = pd->GetValue();
string::size_type last = 0;
string::size_type pos = lines.find('\n');
while (last != string::npos) {
string line = lines.substr(last, pos - last);
if (pos == string::npos)
last = string::npos;
else
last = pos + 1;
pos = lines.find('\n', last);
ofs << attr << line << endl;
}
}
if (!compndWritten) {
if (strlen(mol.GetTitle()) > 0)
snprintf(buffer, BUFF_SIZE, "COMPND %s ",mol.GetTitle());
else
snprintf(buffer, BUFF_SIZE, "COMPND UNNAMED");
ofs << buffer << endl;
}
if (!authorWritten) {
snprintf(buffer, BUFF_SIZE, "AUTHOR GENERATED BY OPEN BABEL %s",BABEL_VERSION);
ofs << buffer << endl;
}
// Write CRYST1 record, containing unit cell parameters, space group
// and Z value (supposed to be 1)
if (pmol->HasData(OBGenericDataType::UnitCell))
{
OBUnitCell *pUC = (OBUnitCell*)pmol->GetData(OBGenericDataType::UnitCell);
if(pUC->GetSpaceGroup()){
string tmpHM=pUC->GetSpaceGroup()->GetHMName();
// Do we have an extended HM symbol, with origin choice as ":1" or ":2" ? If so, remove it.
size_t n=tmpHM.find(":");
if(n!=string::npos) tmpHM=tmpHM.substr(0,n);
snprintf(buffer, BUFF_SIZE,
"CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s 1",
pUC->GetA(), pUC->GetB(), pUC->GetC(),
pUC->GetAlpha(), pUC->GetBeta(), pUC->GetGamma(),
tmpHM.c_str());
}
else
snprintf(buffer, BUFF_SIZE,
"CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s 1",
pUC->GetA(), pUC->GetB(), pUC->GetC(),
pUC->GetAlpha(), pUC->GetBeta(), pUC->GetGamma(),
"P1");
ofs << buffer << endl;
}
// before we write any records, we should check to see if any coord < -1000
// which will cause errors in the formatting
double minX, minY, minZ;
minX = minY = minZ = -999.0f;
FOR_ATOMS_OF_MOL(a, mol)
{
if (a->GetX() < minX)
minX = a->GetX();
if (a->GetY() < minY)
minY = a->GetY();
if (a->GetZ() < minZ)
minZ = a->GetZ();
}
vector3 transV = VZero;
if (minX < -999.0)
transV.SetX(-1.0*minX - 900.0);
if (minY < -999.0)
transV.SetY(-1.0*minY - 900.0);
if (minZ < -999.0)
transV.SetZ(-1.0*minZ - 900.0);
// if minX, minY, or minZ was never changed, shift will be 0.0f
// otherwise, move enough so that smallest coord is > -999.0f
mol.Translate(transV);
OBAtom *atom;
OBResidue *res;
for (i = 1; i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
strncpy(type_name, etab.GetSymbol(atom->GetAtomicNum()), sizeof(type_name));
type_name[sizeof(type_name) - 1] = '\0';
//two char. elements are on position 13 and 14 one char. start at 14
if (strlen(type_name) > 1)
type_name[1] = toupper(type_name[1]);
else
{
char tmp[10];
strncpy(tmp, type_name, 9); // make sure to null-terminate tmp
snprintf(type_name, sizeof(type_name), " %-3s", tmp);
}
if ( (res = atom->GetResidue()) != 0 )
{
het = res->IsHetAtom(atom);
snprintf(the_res,4,"%s",(char*)res->GetName().c_str());
the_res[4] = '\0';
snprintf(type_name,5,"%s",(char*)res->GetAtomID(atom).c_str());
the_chain = res->GetChain();
//two char. elements are on position 13 and 14 one char. start at 14
if (strlen(etab.GetSymbol(atom->GetAtomicNum())) == 1)
{
if (strlen(type_name) < 4)
{
char tmp[10];
strncpy(tmp, type_name, 9); // make sure to null-terminate tmp
snprintf(padded_name, sizeof(padded_name), " %-3s", tmp);
strncpy(type_name,padded_name,4);
type_name[4] = '\0';
}
else
{
/*
type_name[4] = type_name[3];
type_name[3] = type_name[2];
type_name[2] = type_name[1];
type_name[1] = type_name[0];
type_name[0] = type_name[4];
*/
type_name[4] = '\0';
}
}
res_num = res->GetNum();
}
else
{
strcpy(the_res,"UNK");
the_res[3] = '\0';
snprintf(padded_name,sizeof(padded_name), "%s",type_name);
strncpy(type_name,padded_name,4);
type_name[4] = '\0';
res_num = 1;
}
element_name = etab.GetSymbol(atom->GetAtomicNum());
int charge = atom->GetFormalCharge();
char scharge[3] = { ' ', ' ', '\0' };
if(0 != charge)
{
snprintf(scharge, 3, "%+d", charge);
char tmp = scharge[1];
scharge[1] = scharge[0];
scharge[0] = tmp;
}
snprintf(buffer, BUFF_SIZE, "%s%5d %-4s %-3s %c%4d %8.3f%8.3f%8.3f 1.00 0.00 %2s%2s\n",
het?"HETATM":"ATOM ",
i,
type_name,
the_res,
the_chain,
res_num,
atom->GetX(),
atom->GetY(),
atom->GetZ(),
element_name,
scharge);
ofs << buffer;
}
OBAtom *nbr;
vector<OBBond*>::iterator k;
for (i = 1; i <= mol.NumAtoms(); i ++)
{
atom = mol.GetAtom(i);
if (atom->GetValence() == 0)
continue; // no need to write a CONECT record -- no bonds
snprintf(buffer, BUFF_SIZE, "CONECT%5d", i);
ofs << buffer;
// Write out up to 4 real bonds per line PR#1711154
int currentValence = 0;
for (nbr = atom->BeginNbrAtom(k);nbr;nbr = atom->NextNbrAtom(k))
{
snprintf(buffer, BUFF_SIZE, "%5d", nbr->GetIdx());
ofs << buffer;
if (++currentValence % 4 == 0) {
// Add the trailing space to finish this record
ofs << " \n";
// write the start of a new CONECT record
snprintf(buffer, BUFF_SIZE, "CONECT%5d", i);
ofs << buffer;
}
}
// Add trailing spaces
int remainingValence = atom->GetValence() % 4;
for (int count = 0; count < (4 - remainingValence); count++) {
snprintf(buffer, BUFF_SIZE, " ");
ofs << buffer;
}
ofs << " \n";
}
snprintf(buffer, BUFF_SIZE, "MASTER 0 0 0 0 0 0 0 0 ");
ofs << buffer;
snprintf(buffer, BUFF_SIZE, "%4d 0 %4d 0\n",mol.NumAtoms(),mol.NumAtoms());
ofs << buffer;
ofs << "END\n";
if (model_num) {
ofs << "ENDMDL" << endl;
}
return(true);
}
bool ChemDrawXMLFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
static const xmlChar C_MOLECULE[] = "fragment";
static const xmlChar C_CDXML[] = "CDXML";
static const xmlChar C_BONDLENGTH[] = "BondLength";
static const xmlChar C_PAGE[] = "page";
static const xmlChar C_ATOM[] = "n";
static const xmlChar C_BOND[] = "b";
static const xmlChar C_ID[] = "id";
static const xmlChar C_CHARGE[] = "Charge";
static const xmlChar C_COORDS[] = "p";
static const xmlChar C_ELEMENT[] = "Element";
static const xmlChar C_ORDER[] = "Order";
static const xmlChar C_BEGIN[] = "B";
static const xmlChar C_END[] = "E";
static const xmlChar C_DISPLAY[] = "Display";
_pxmlConv = XMLConversion::GetDerived(pConv,false);
if(!_pxmlConv)
return false;
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
OBMol &mol = *pmol;
OBBond *pbond;
vector<OBBond*>::iterator j;
if(_pxmlConv->GetOutputIndex() == 1)
{
xmlTextWriterStartDocument(writer(), NULL, NULL, NULL);
xmlTextWriterWriteDTD(writer(), BAD_CAST "CDXML", NULL, BAD_CAST "http://www.camsoft.com/xml/cdxml.dtd", NULL);
xmlTextWriterStartElement(writer(), C_CDXML);
xmlTextWriterWriteFormatAttribute(writer(), C_BONDLENGTH , "30");
xmlTextWriterStartElement(writer(), C_PAGE); // put everything on one page
// now guess the average bond size for the first molecule and scale to 30.
_scale = 0.;
if (mol.NumBonds())
{
for (pbond = mol.BeginBond(j); pbond; pbond = mol.NextBond(j))
_scale += pbond->GetLength();
_scale /= mol.NumBonds();
}
else
_scale = 1.; // FIXME: what happens if the molecule has no bond?
_scale = 30. / _scale;
_offset = 0;
}
xmlTextWriterStartElement(writer(), C_MOLECULE);
OBAtom *patom;
vector<OBAtom*>::iterator i;
int n;
for (patom = mol.BeginAtom(i); patom; patom = mol.NextAtom(i))
{
xmlTextWriterStartElement(writer(), C_ATOM);
xmlTextWriterWriteFormatAttribute(writer(), C_ID , "%d", patom->GetIdx() + _offset);
xmlTextWriterWriteFormatAttribute(writer(), C_COORDS , "%f %f", patom->GetX() * _scale, patom->GetY() * _scale);
n = patom->GetAtomicNum();
if (n != 6)
{
xmlTextWriterWriteFormatAttribute(writer(), C_ELEMENT , "%d", n);
}
n = patom->GetFormalCharge();
if (n != 0)
{
xmlTextWriterWriteFormatAttribute(writer(), C_CHARGE , "%d", n);
}
xmlTextWriterEndElement(writer());
}
for (pbond = mol.BeginBond(j); pbond; pbond = mol.NextBond(j))
{
xmlTextWriterStartElement(writer(), C_BOND);
patom = pbond->GetBeginAtom();
xmlTextWriterWriteFormatAttribute(writer(), C_BEGIN , "%d", patom->GetIdx() + _offset);
patom = pbond->GetEndAtom();
xmlTextWriterWriteFormatAttribute(writer(), C_END , "%d", patom->GetIdx() + _offset);
n = pbond->GetBO();
if (n != 1)
{
xmlTextWriterWriteFormatAttribute(writer(), C_ORDER , "%d", n);
}
if (pbond->IsHash())
xmlTextWriterWriteFormatAttribute(writer(), C_DISPLAY , "WedgeBegin");
else if (pbond->IsWedge())
xmlTextWriterWriteFormatAttribute(writer(), C_DISPLAY , "WedgedHashEnd");
xmlTextWriterEndElement(writer());
}
_offset += mol.NumAtoms ();
xmlTextWriterEndElement(writer());//molecule
//TODO: Writing property block
if(_pxmlConv->IsLast())
{
xmlTextWriterEndDocument(writer()); // page
xmlTextWriterEndDocument(writer()); //document
OutputToStream();
}
return true;
}
bool OBDepict::DrawMolecule(OBMol *mol)
{
if (!d->painter)
return false;
d->mol = mol;
double width=0.0, height=0.0;
OBAtom *atom;
OBBondIterator j;
OBAtomIterator i;
if(mol->NumAtoms()>0) {
// scale bond lengths
double bondLengthSum = 0.0;
for (OBBond *bond = mol->BeginBond(j); bond; bond = mol->NextBond(j))
bondLengthSum += bond->GetLength();
const double averageBondLength = bondLengthSum / mol->NumBonds();
const double f = mol->NumBonds() ? d->bondLength / averageBondLength : 1.0;
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
atom->SetVector(atom->GetX() * f, atom->GetY() * f, 0.0);
// find min/max values
double min_x, max_x;
double min_y, max_y;
atom = mol->BeginAtom(i);
min_x = max_x = atom->GetX();
min_y = max_y = atom->GetY();
for (atom = mol->NextAtom(i); atom; atom = mol->NextAtom(i)) {
min_x = std::min(min_x, atom->GetX());
max_x = std::max(max_x, atom->GetX());
min_y = std::min(min_y, atom->GetY());
max_y = std::max(max_y, atom->GetY());
}
const double margin = 40.0;
// translate all atoms so the bottom-left atom is at margin,margin
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
atom->SetVector(atom->GetX() - min_x + margin, atom->GetY() - min_y + margin, 0.0);
width = max_x - min_x + 2*margin;
height = max_y - min_y + 2*margin;
//d->painter->SetPenWidth(d->penWidth);
//d->painter->SetPenColor(d->pen));
//d->painter->SetFillColor(OBColor("black"));
}
d->painter->NewCanvas(width, height);
// draw bonds
if(d->options & genWedgeHash)
d->SetWedgeAndHash(mol);
for (OBBond *bond = mol->BeginBond(j); bond; bond = mol->NextBond(j)) {
OBAtom *begin = bond->GetBeginAtom();
OBAtom *end = bond->GetEndAtom();
if((d->options & internalColor) && bond->HasData("color"))
d->painter->SetPenColor(OBColor(bond->GetData("color")->GetValue()));
else
d->painter->SetPenColor(d->bondColor);
if (bond->IsWedge()) {
d->DrawWedge(begin, end);
} else if (bond->IsHash()) {
d->DrawHash(begin, end);
} else if (!bond->IsInRing()) {
d->DrawSimpleBond(begin, end, bond->GetBO());
}
}
// draw ring bonds
std::vector<OBRing*> rings(mol->GetSSSR());
OBBitVec drawnBonds;
for (std::vector<OBRing*>::iterator k = rings.begin(); k != rings.end(); ++k) {
OBRing *ring = *k;
std::vector<int> indexes = ring->_path;
vector3 center(VZero);
for (std::vector<int>::iterator l = indexes.begin(); l != indexes.end(); ++l) {
center += mol->GetAtom(*l)->GetVector();
}
center /= indexes.size();
for (unsigned int l = 0; l < indexes.size(); ++l) {
OBAtom *begin = mol->GetAtom(indexes[l]);
OBAtom *end;
if (l+1 < indexes.size())
end = mol->GetAtom(indexes[l+1]);
else
end = mol->GetAtom(indexes[0]);
OBBond *ringBond = mol->GetBond(begin, end);
if (drawnBonds.BitIsSet(ringBond->GetId()))
continue;
if((d->options & internalColor) && ringBond->HasData("color"))
d->painter->SetPenColor(OBColor(ringBond->GetData("color")->GetValue()));
else
d->painter->SetPenColor(d->bondColor);
d->DrawRingBond(begin, end, center, ringBond->GetBO());
drawnBonds.SetBitOn(ringBond->GetId());
}
}
// draw atom labels
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i)) {
double x = atom->GetX();
double y = atom->GetY();
int alignment = GetLabelAlignment(atom);
bool rightAligned = false;
switch (alignment) {
case TopRight:
case CenterRight:
case BottomRight:
rightAligned = true;
default:
break;
}
if((d->options & internalColor) && atom->HasData("color"))
d->painter->SetPenColor(OBColor(atom->GetData("color")->GetValue()));
else if(d->options & bwAtoms)
d->painter->SetPenColor(d->bondColor);
else
d->painter->SetPenColor(OBColor(etab.GetRGB(atom->GetAtomicNum())));
//charge and radical
int charge = atom->GetFormalCharge();
int spin = atom->GetSpinMultiplicity();
if(charge || spin) {
OBFontMetrics metrics = d->painter->GetFontMetrics("N");
double yoffset = d->HasLabel(atom) ? 0.4 * metrics.height : 0.0;
switch (GetLabelAlignment(atom)) {
case TopCenter:
case TopRight:
case TopLeft:
case CenterLeft:
case CenterRight:
yoffset = - 1.2 * metrics.height;
}
stringstream ss;
if(charge) {
if(abs(charge)!=1)
ss << abs(charge);
ss << (charge>0 ? "+" : "-") ;
}
if(spin) {
ss << (spin==2 ? "." : "..");
yoffset += 0.5 * metrics.height;
}
if(spin || charge<0)
d->painter->SetFontSize(2 * metrics.fontSize);
d->painter->DrawText(x-0.4*metrics.width, y-yoffset, ss.str());
d->painter->SetFontSize(metrics.fontSize);//restore
}
if (atom->IsCarbon()) {
if(!(d->options & drawAllC))
{
if (atom->GetValence() > 1)
continue;
if ((atom->GetValence() == 1) && !(d->options & drawTermC))//!d->drawTerminalC)
continue;
}
}
stringstream ss;
AliasData* ad = NULL;
if(d->aliasMode && atom->HasData(AliasDataType))
ad = static_cast<AliasData*>(atom->GetData(AliasDataType));
//For unexpanded aliases use appropriate form of alias instead of element symbol, Hs, etc
if(ad && !ad->IsExpanded())
{
ss <<ad->GetAlias(rightAligned);
OBColor aliasColor = !ad->GetColor().empty() ? ad->GetColor() : d->bondColor;
d->painter->SetPenColor(aliasColor);
}
else {
const char* atomSymbol;
if(atom->IsHydrogen() && atom->GetIsotope()>1)
atomSymbol = atom->GetIsotope()==2 ? "D" : "T";
else
atomSymbol = etab.GetSymbol(atom->GetAtomicNum());
unsigned int hCount = atom->ImplicitHydrogenCount();
// rightAligned:
// false CH3
// true H3C
if (hCount && rightAligned)
ss << "H";
if ((hCount > 1) && rightAligned)
ss << hCount;
ss << atomSymbol;
if (hCount && !rightAligned)
ss << "H";
if ((hCount > 1) && !rightAligned)
ss << hCount;
}
d->DrawAtomLabel(ss.str(), alignment, vector3(x, y, 0.0));
}
return true;
}
bool BGFFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
vector<OBAtom*>::iterator i;
int max_val;
OBAtom *atom;
char buffer[BUFF_SIZE];
char elmnt_typ[8], dreid_typ[8], atm_sym[16], max_val_str[8];
mol.Kekulize();
ofs << "BIOGRF 200\n";
snprintf(buffer, BUFF_SIZE, "DESCRP %s\n",mol.GetTitle());
ofs << buffer;
snprintf(buffer, BUFF_SIZE, "REMARK BGF file created by Open Babel %s\n",BABEL_VERSION);
ofs << "FORCEFIELD DREIDING \n";
// write unit cell if available
if (mol.HasData(OBGenericDataType::UnitCell))
{
OBUnitCell *uc = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
// e.g. CRYSTX 49.30287 49.23010 25.45631 90.00008 89.99995 57.10041
snprintf(buffer, BUFF_SIZE,
"CRYSTX%12.5f%12.5f%12.5f%12.5f%12.5f%12.5f",
uc->GetA(), uc->GetB(), uc->GetC(),
uc->GetAlpha() , uc->GetBeta(), uc->GetGamma());
ofs << buffer << "\n";
}
ofs << "FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5)\n";
ttab.SetFromType("INT");
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
strncpy(elmnt_typ,etab.GetSymbol(atom->GetAtomicNum()), 7); // make sure to null-terminate
elmnt_typ[sizeof(elmnt_typ) - 1] = '0';
ToUpper(elmnt_typ);
ttab.SetToType("DRE");
ttab.Translate(dreid_typ,atom->GetType());
ttab.SetToType("HAD");
ttab.Translate(max_val_str,atom->GetType());
max_val = atoi(max_val_str);
if (max_val == 0)
max_val = 1;
snprintf(atm_sym,16,"%s%d",elmnt_typ,atom->GetIdx());
snprintf(buffer,BUFF_SIZE,"%6s %5d %-5s %3s %1s %5s%10.5f%10.5f%10.5f %-5s%3d%2d %8.5f\n",
"HETATM",
atom->GetIdx(),
atm_sym,
"RES",
"A",
"444",
atom->GetX(),
atom->GetY(),
atom->GetZ(),
dreid_typ,
max_val,
0,
atom->GetPartialCharge());
ofs << buffer;
}
ofs<< "FORMAT CONECT (a6,12i6)\n\n";
OBAtom *nbr;
vector<OBBond*>::iterator j;
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
if (atom->GetValence())
{
snprintf(buffer,BUFF_SIZE,"CONECT%6d",atom->GetIdx());
ofs << buffer;
for (nbr = atom->BeginNbrAtom(j);nbr;nbr = atom->NextNbrAtom(j))
{
snprintf(buffer,BUFF_SIZE,"%6d",nbr->GetIdx());
ofs << buffer;
}
ofs << endl;
snprintf(buffer,BUFF_SIZE,"ORDER %6d",atom->GetIdx());
ofs << buffer;
for (nbr = atom->BeginNbrAtom(j);nbr;nbr = atom->NextNbrAtom(j))
{
snprintf(buffer,BUFF_SIZE,"%6d",(*j)->GetBO());
ofs << buffer;
}
ofs << endl;
}
ofs << "END" << endl;
return(true);
}
